What are some of the latest/advanced tools for ribo-seq analysis? If anyone here with experience in ribo-seq can guide me through or recommend me some tutorials that would be really helpful. I'm particularly interested in annotation of small ORFs (smORFs) in my data.
Hopefully this is somewhat helpful. This paper explains why ORF calling is still a very variable process that depends heavily on your data quality. Nonetheless, you can still get a lot of information on non-canonical translation from running these tools. RibORF, PRICE, RiboTricer are all popular. In my opinion it is important to verify ORF calls manually by looking at the subcodon profiles for the data. Trips-Viz has ORF calling via a user interface that makes this relatively easy as it provides direct links to the translated ORFs and allows you to compare calls with data from publicly available datasets.
I have a roughly curated list of other tools that offer ORF calling here.